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High Throughput Mining and Characterization of Microsatellites from Common Carp Genome

文献类型: 外文期刊

作者: Ji, Peifeng 1 ; Zhang, Yan 1 ; Li, Chao 2 ; Zhao, Zixia 1 ; Wang, Jian 1 ; Li, Jiongtang 1 ; Xu, Peng 1 ; Sun, Xiaowen 1 ;

作者机构: 1.Chinese Acad Fishery Sci, Ctr Appl Aquat Genom, Beijing 100141, Peoples R China

2.Chinese Acad Fishery Sci, Heilongjiang Fishery Res Inst, Harbin 150070, Peoples R China

关键词: microsatellites;common carp;genome;linkage map;BAC end sequences

期刊名称:INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES ( 影响因子:5.923; 五年影响因子:6.132 )

ISSN: 1661-6596

年卷期: 2012 年 13 卷 8 期

页码:

收录情况: SCI

摘要: In order to supply sufficient microsatellite loci for high-density linkage mapping, whole genome shotgun (WGS) sequences of the common carp (Cyprinus carpio) were assembled and surveyed for microsatellite identification. A total of 79,014 microsatellites were collected which were harbored in 68,827 distinct contig sequences. These microsatellites were characterized in the common carp genome. Information of all microsatellites, including previously published BAC-based microsatellites, was then stored in a MySQL database, and a web-based database interface (http://genomics.cafs.ac.cn/ssrdb) was built for public access and download. A total of 3,110 microsatellites, including 1,845 from WGS and 1,265 from BAC end sequences (BES), were tested and genotyped on a mapping family with 192 individuals. A total of 963 microsatellites markers were validated with polymorphism in the mapping family. They will soon be used for high-density linkage mapping with a vast number of polymorphic SNP markers.

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